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Donatello, April O'Neil, and Harold Lillja worked at Harold's Laboratory on an Interspatial Teleportation Unit based on the schematics of their ally Fugitoid. After some tinkering, Donatello believed all "known discrepancies" were worked out. He conducted a small test and teleported to and from the parking lot by Harold's lab. However, he wanted to a do a real test and gathered everyone so they could teleport to The Lair and surprise Master Splinter. However, Harold touched a switch marked "Spatial Dimension Do Not Touch" while swatting a fly. After returning from the Ghostbusters' dimension, Donatello was mortally wounded. His comrades managed to transfer his consciousness into a robot named Metalhead. It felt like a dream, sometimes clear and sometimes fuzzy. [3] Donatello struggled with identity when he was in Metalhead. He could feel his own body was hollow yet part of him felt warm. At one point, he remembered being in a garden. [4] Eventually, Donatello was returned to his fully healed body.

Stuck in another dimension, Donatello confirmed his calculations through GPS but they were not standing in their lair. They were in the Emmanuel Baptist Church and interrupted a wedding. To compound the matter, he refused to admit they were being attacked by a ghost, Chi-You. Despite being shot at, Donatello was really interested at a closer look at the Ghostbusters' equipment. Rather than go look for Casey, Donatello believed it would be for the better to accept the Ghostbusters' help and make use of their technology. He explained the incident that led to their arrival in another dimension then showed Egon Spengler and Ray Stantz the schematics for the Interspatial Teleportation Unit. At the Firehouse, Donatello was smitten with all their equipment but was took issue with the existence of ghosts. He even thought Chi-You was a possible extraterrestrial parasitic creature. Donatello's skepticism continued as Ray warded Slimer with a copy of Fairfax's Demonologia. Ray took him down to the basement. Along the way, Ray tried to reason with Donatello by distilling the afterlife to a science. Donatello was amazed by the Containment Unit and regarded it as an impressive piece of engineering. He was further impressed upon inspecting the unit's self-contained power source and verified it could be used to fuel a new Interspatial Teleportation Unit. When faced with cramming weeks worth of work into 72 hours or a lead on Chi-You and Casey, Donatello agreed with pursuing the latter. Ray outfitted Donatello with his spare Proton Pack.

After observing Chi-You and his connection with his thralls, Donatello hypothesized a low-voltage pulse instead of a Proton Stream would break the tether. Egon and Ray agreed and went to work on modifying Arm Mounted Proton Packs. While the others confronted Chi-You again, Donatello started working on building another Interspatial Teleportation Unit with Egon, Ray, and April.

After several hours, Egon and Donatello made strides in recreating a functional teleportation unit in the Firehouse basement. Donatello inquired about the proximity alarm but Egon pushed on and the teleportation unit was powered on. However, it became apparent Egon miscalculated the intense drain the teleportation unit would have on the containment grid's power supply. They rushed to stabilize the grid before it ruptured and caused a horrific explosion. Egon rerouted power from a panel and Donatello located several blown boards in the Containment Unit's control panel. On Egon's instruction, Donatello grabbed a tool that looked like a medieval torture device and worked on the guts of the power supply. They managed to avert disaster while the others captured Chi-You. Donatello was more than ready to return home where reincarnation was as far as things went.

The Turtles were just about to leave Dimension X then The Collectors appeared. At first, they mistook the Collectors for natives of Dimension X until they took on grotesque forms of the Turtles and attacked. The Turtles soon realized they couldn't make physical contact with them. Using his quick thinking and eidetic memory, Donatello reset the transporter's controls to the coordinates of the Ghostbusters' dimension and jumped through the portal to get help. He arrived on the second floor of the Firehouse and explained the situation to Egon and Ray. The Collectors manifested and grabbed Donatello. Donatello was reunited with the others in the Collectors' Limbo. Darius Dun appeared to the Turtles and revealed his part in summoning The Collectors to get revenge on Splinter for his execution.

To their surprise, the Turtles were found by Ray, Peter, and Winston. Michelangelo cheered Donatello for coming through and even Raphael complimented him. However, Ray instructed Donatello to put on an Experimental Mental Communications Device then walk through the open portal back to the Firehouse. The others paired off and jumped to random dimensions. Donatello was greeted by Egon in the basement. As they went up to the third floor, Donatello realized the device was temporary camouflage from the Collectors. Egon admitted Donatello was better equipped to answer questions on transdimensional mechanics than Ray and together, they were going to work on a way to permanently trap the Collectors. Egon then explained the others were a distraction to further slow the Collectors down. Donatello could believe they figured out remote portal access and the helmet modification in minutes. To Donatello's dismay, Egon revealed roughly three weeks passed since he crossed over. Donatello admitted it's been a "month of long days" for himself and the others and he was ready for that to be over. Egon turned his attention to a completed simulation. They had less than a day's time before the Collectors were projected to find the others. Donatello was ready to get to work.

Donatello admitted he was amazed with how much Egon and Ray modified his original design for the teleportation unit as well as with inventing the access bands. Egon admitted a drawback of the technology was it stirred up P.K.E. and attracted ghosts. Egon revealed the idea was to combine the portal technology with the Trap to directly transport the four Collectors into the Containment Unit. He needed Donatello's help to recreate the original technology rather than spend days on trial and error because he and Ray modified their unit immensely. And Ray might have lost the notes Donatello left behind when Egon was temporarily dead. [5][6][7] Before Donatello could question Egon about being dead, data from the dimensional breach alarm allowed Egon's simulation to more accurately predict when the Collectors would capture the others. They had even less time. Donatello got an idea on how to prevent the Collectors from escaping before they could trap them. While they worked on the Trap-Gate, Donatello believed they had to boost the power of the Trap-Gate by a factor of three for it to be a one-way trip for the Collectors. Donatello's Communications Device suddenly went haywire and he suffered neural confusion with Winston. His speech pattern and inflections began to resemble Winston's. Likewise, across dimensions, Winston's began to resemble Donatello's. Donatello observed it felt like his soul was in two places again. Egon moved to adjust the sensitivity when he realized Donatello said "again." He briefly felt like his brain was everywhere at once and gleaned the Collectors breaching dimensions. Janine entered the room with a delivery from Kung Fu Hustle Supply Emporium. She was concerned to see Donatello in distress. Egon admitted it was partly his fault but Donatello downplayed it. Janine suggested he sit down for a bit but Donatello insisted there was no time for that because he could feel the Collectors searching for the Turtles then revealed his idea was to build proton-powered ninja arsenal based on the Turtles' primary weapons.

Egon and Donatello went to the Warehouse to use the ionized glass enclosure to test their prototypes. Egon cautioned Donatello the glass may not be able to withstand too many hints from his Proton Weapon then placed a Trap into a slot and released a Mouth Critter Ghost into the enclosure with Donatello. Donatello asked Egon to humor his request and talk about what it was like being dead. Egon was surprised and asked if wanted to just focus on the matter at hand. He offered to provide copies of all the tests he took upon his return. Beyond that, Egon didn't think there was much to tell. Donatello explained talking while fighting was something he did with his brothers and found it comforting. He added he found the ghost terrifying and asked Egon to humor him. Egon replied he experienced a feeling of peace and was able to fully focus on his thoughts then asked Donatello what he meant by his soul being in two places. Donatello explained he was mortally wounded and his consciousness was temporarily placed in a robot shell. He likened it to a dream, sometimes clear and sometimes fuzzy. Donatello managed to hit the ghost with his proton-powered staff. The ghost retaliated and knocked him across the enclosure. The force and Donatello's shell made a crack in the glass. Donatello decided to try the Trap-Gate but soon realized they miscalculated the power needed. Egon grabbed the Trap but remembered there was a safety in place that kept the door locked to keep any active ghosts contained. He asked Donatello to stall but noticed he sounded like Winston again. Egon instructed him not to let himself drift then asked him to continue with his story. Donatello felt like when he was in the robot, it was him but it wasn't. He recalled his body was hollow but part of him felt warm. Lastly, he remembered being in a garden. Egon ripped out several red wires and unlocked the door. He threw out the Trap and recaptured the ghost. Egon concluded they had to boost the Trap-Gate's power considerably then inquired if he ever felt guilty about coming back. Donatello replied he shouldn't but admitted he did and read up on Survivor's Guilt even though he knew that wasn't it. They rushed back to the Firehouse to do their final modifications.

On page 18 of Teenage Mutant Ninja Turtles/Ghostbusters Volume 2 Issue #2, Donatello notes his soul was once in two places before. In the Teenage Mutant Ninja Turtles comic, after his soul was returned to his healed body, Donatello discovered a digital copy of his soul was still in the Metalhead robot.

On page 14 of Teenage Mutant Ninja Turtles/Ghostbusters Volume 2 Issue #3, Donatello mentions remembering being in a garden. Donatello met his mother Tang Shen in a garden in Teenage Mutant Ninja Turtles #45 and was counseled on choosing to go to the light or the darkness after he died.